DIVA: Natural Navigation inside 3D Images Using Virtual Reality

Autor: Bassam Hajj, Stéphane Fournier, Clément Caporal, Mohamed El Beheiry, Sébastien Doutreligne, Oumaima Sliti, Charlotte Godard, Jean-Baptiste Masson, Valentin Marcon, Maxime Dahan, Cécilia Ostertag
Přispěvatelé: Physico-Chimie-Curie (PCC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Décision et processus Bayesiens - Decision and Bayesian Computation, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), We acknowledge funding from the Institut Pasteur (J.B.M), The Institut Curie (M.D.), Paris Science Lettres (M.D., J.B.M.) the sponsorship of CRPCEN (J.B.M), the sponsorship of Gilead-Science (J.B.M.), sponsorship of the fondation EDF (J.B.M.), the ANR-17-CE23-0016 TRamWAy (J.B.M),the INCEPTION project (PIA/ANR-16-CONV-0005, OG) (J.B.M), the 'Investissements d’avenir' program under the management of Agence Nationale de la Recherche, reference ANR-19-P3IA-0001 (PRAIRIE 3IA Institute)., We thank Kurt Sailor (Institut Pasteur), Richard Weinberg (University of North Carolina), Thomas Rubin and Jean-Ren Huynh (Collège de France) for the image datasets provided to generate the figures, We thank all the research teams from Institut Curie, Institut Pasteur, Collège de France who tested the DIVA software and provided feedbacks that have strongly influence the development of the software., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-17-CE23-0016,TRamWAy,L'Analyseur Automatique de Marches Aléatoires Biomoléculaires: La Science des molécules uniques à l'époque des données massives(2017), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Décision et processus Bayesiens / Decision and Bayesian Computation, Département de Neuroscience - Department of Neuroscience
Jazyk: angličtina
Rok vydání: 2020
Předmět:
Computer science
[SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging
Data treatment
ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION
Image processing
Context (language use)
Stereoscopy
02 engineering and technology
Virtual reality
law.invention
User-Computer Interface
03 medical and health sciences
[SPI]Engineering Sciences [physics]
0302 clinical medicine
Data visualization
Imaging
Three-Dimensional
Software
Match moving
Structural Biology
law
Computer graphics (images)
0202 electrical engineering
electronic engineering
information engineering
Human-in-the-Loop
Humans
[INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC]
Molecular Biology
ComputingMilieux_MISCELLANEOUS
030304 developmental biology
[PHYS]Physics [physics]
0303 health sciences
Microscopy
business.industry
Virtual Reality
020207 software engineering
Volume rendering
Visualization
Diva
business
030217 neurology & neurosurgery
Data Visualisation
Zdroj: Journal of Molecular Biology
Journal of Molecular Biology, 2020, 432 (16), pp.4745-4749. ⟨10.1016/j.jmb.2020.05.026⟩
Journal of Molecular Biology, Elsevier, 2020, 432 (16), pp.4745-4749. ⟨10.1016/j.jmb.2020.05.026⟩
ISSN: 0022-2836
1089-8638
Popis: As three-dimensional microscopy becomes commonplace in biological re-search, there is an increasing need for researchers to be able to view experimental image stacks in a natural three-dimensional viewing context. Through stereoscopy and motion tracking, commercial virtual reality headsets provide a solution to this important visualization challenge by allowing researchers to view volumetric objects in an entirely intuitive fashion. With this motivation, we present DIVA, a user-friendly software tool that automatically creates detailed three-dimensional reconstructions of raw experimental image stacks that are integrated in virtual reality. In DIVA’s immersive virtual environment, users can view, manipulate and perform volumetric measurements on their microscopy images as they would to real physical objects. In contrast to similar solutions, our software provides high-quality volume rendering with native TIFF file compatibility. We benchmark the software with diverse image types including those generated by confocal, light-sheet and electron microscopy. DIVA is available at https://diva.pasteur.fr and will be regularly updated.
Databáze: OpenAIRE
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